Once you have finished all the stages (including the castle underground area, if you went that route), you must be feeling pretty good about yourself. Since you have all the treasures and he's a fiend, Flintheart Glomgold kidnaps Webby and demands that you come to his ship with your treasures in hand if you mean to rescue her.

This final stage is actually just a repeat of the Bermuda stage, with a different route to the end. From the start, head to the right. There are no enemies, and you can no longer access the lower reaches of the ship as you could previously. Instead, just keep pushing right. Where before a metal door barred your way, you'll now find the path cleared to a rope. Climb up to its top, then walk to the right through a narrow corridor, into the boss chamber.
D-1000
Rather than relying on his own muscle, Scroog's old nemesis calls out a robot named the D-1000. This beast is the other 'tough' boss in the game, and you may want to have a cake with you just in case.
His basic strategy is to take small steps toward you, send a mechanical arm to the ceiling, then kick at you with a long-range kick. Try and stay on the opposite side of the screen. Let him move toward you and, when he's near, hop out as he starts to walk toward you. This should allow you to get in the air over him before his arm has properly extended, and you can pogo on his head.
You'll have to repeat this five times to beat him, which means switching screen sides with him the same number of times. On average, it's safest to let him approach four to five times from the opposite side of the screen before rushing in to attack. Just keep your head and you'll win.
NEXT: Conclusion